| Variant ID: vg0621393859 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 21393859 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
TCCGTTCTTCGGCATGCCAGCGCACAAGCTTAGCTTGTTCCTTGTTCGCAAACATTCTCTTCATGCGCTCCGCAATTGGGAGATACCACACCACCTTTGC[T/G]
GGGCCTCCCCTCTTTGACTTACTTTCTTCACCTTCACTCTTTGCTCGTTTGTATCTTGATGCCCCACAGATAGGGCAGACATCCAAGTCAGCGTATTCCT
AGGAATACGCTGACTTGGATGTCTGCCCTATCTGTGGGGCATCAAGATACAAACGAGCAAAGAGTGAAGGTGAAGAAAGTAAGTCAAAGAGGGGAGGCCC[A/C]
GCAAAGGTGGTGTGGTATCTCCCAATTGCGGAGCGCATGAAGAGAATGTTTGCGAACAAGGAACAAGCTAAGCTTGTGCGCTGGCATGCCGAAGAACGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.30% | 0.00% | 2.56% | 97.12% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 0.40% | 99.13% | NA |
| All Japonica | 1512 | 0.10% | 0.00% | 7.01% | 92.92% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.00% | 99.83% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.86% | 98.06% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.11% | 99.23% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 0.76% | 99.11% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 1.69% | 98.31% | NA |
| Tropical Japonica | 504 | 0.20% | 0.00% | 10.91% | 88.89% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 15.77% | 84.23% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 4.44% | 94.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0621393859 | T -> G | LOC_Os06g36440.1 | synonymous_variant ; p.Pro268Pro; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0621393859 | T -> DEL | LOC_Os06g36440.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |